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Crystal structure of the N-terminal domain of E.coli YbgF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5 0.1M SODIUM ACETATE PH 5.0, 10% PEG4000, 7.5% DIOXANE
Crystal Properties Matthews coefficient Solvent content 2.07 40.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.737 α = 90 b = 41.382 β = 90 c = 237.697 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC CCD 2009-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.48 50 100 0.05 50.1 7.8 26790 2 28.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.48 2.52 100 0.09 23.7 7.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT NONE 2.48 39.62 13919 737 99.9 0.21709 0.21257 0.2105 0.30223 0.2956 RANDOM 21.087
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.03 0.02 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.672 r_dihedral_angle_4_deg 22.303 r_dihedral_angle_3_deg 18.542 r_dihedral_angle_1_deg 5.089 r_scangle_it 4.979 r_scbond_it 2.807 r_mcangle_it 1.562 r_angle_refined_deg 1.526 r_mcbond_it 0.741 r_chiral_restr 0.101
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.672 r_dihedral_angle_4_deg 22.303 r_dihedral_angle_3_deg 18.542 r_dihedral_angle_1_deg 5.089 r_scangle_it 4.979 r_scbond_it 2.807 r_mcangle_it 1.562 r_angle_refined_deg 1.526 r_mcbond_it 0.741 r_chiral_restr 0.101 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3208 Nucleic Acid Atoms Solvent Atoms 94 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling SHELX phasing